Correct: 1. What they were really interested in was where to get money from. 2. The only thing they were really interested in was where to get money from.

The minimal changes to your sentences to make them correct are "What they were only interested in was where we get money for it from" and "The only thing they were really interested in was where we get money for it from". But I would say "All they were interested in was how we were going to pay for it".

The only thing they were interested in was where they would get the money. (I don't think it's correct to end a sentence with a preposition)

in my opinion, first sentence is correct, but the second one: The only thing, they were really interested in, was where do we get money for it from. What they was really interested in was only where do we get money for it from.(I dont know which version of the first one is nativer)

The only thing they were really interested in was where do they get the money?